Help with AWK and Scripting! Post: 302445626

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Top Forums Shell Programming and Scripting Help with AWK and Scripting! Post 302445626 by SriJit on Monday 16th of August 2010 11:12:15 AM

08-16-2010

Registered User

Incorrect Ouput

Hi Agama,

I ran yoyour second code. It gives me the wrong output. It even prints the texts in the input.

Here is a sample input,

Code:

#### ACGG_NNNP.pairwiseRMSDs.txt
#### Output from pdb_extract.py
#### Created 2010-08-12 13:59:31.122708

5 structures aligned

1OSW_0002_ACGG_NNNP_A_10_13.pdb.pdb most representative structure of pool
 with lowest average pair-wise RMSD of 0.81

    Mean global RMSD: 0.91  (0.81 to 0.98A)
 Mean global bb RMSD: 0.72  (0.65 to 0.82A)

                                 Avg  Avgbb  Pair-Wise RMSD Matrix:
Structure:                       RMSD RMSD  (Top-Right=Heavy atom alignment, Bottom-Left=Backbone atom alignment)
-------------------------------  ---- ----   0_13 0_13 0_13 0_13 0_13
1OSW_0002_ACGG_NNNP_A_10_13.pdb  0.81 0.65  [     0.84 0.77 0.95 0.70]
1OSW_0005_ACGG_NNNP_A_10_13.pdb  0.85 0.76  [0.85      1.01 0.59 0.94]
1OSW_0015_ACGG_NNNP_A_10_13.pdb  0.98 0.68  [0.43 0.83      1.10 1.04]
1OSW_0019_ACGG_NNNP_A_10_13.pdb  0.95 0.82  [0.91 0.51 0.94      1.14]
1OSW_0021_ACGG_NNNP_A_10_13.pdb  0.95 0.67  [0.42 0.83 0.52 0.91     ]

END

Can you please try to run the code for this and see if it works perfectly with just printing the matrix with 0 inserted in the spaces along the diagonal? If not can you make what changes I should make to get that output? It is 5*5 matrix in the above input. There is space along the diagonal.

Thanks,
Srijit

Last edited by Scott; 08-17-2010 at 03:49 AM.. Reason: Code tags, please...

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LEARN ABOUT DEBIAN

g_morph

g_morph(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_morph(1)

NAME

       g_morph - linear interpolation of conformations

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_morph	-f1  conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n index.ndx -[no]h -[no]version -nice int -[no]w -xvg enum -ninterm
       int -first real -last real -[no]fit

DESCRIPTION

	g_morph does a linear interpolation of conformations in order to create intermediates. Of course these are completely unphysical, but that
       you  may  try  to  justify  yourself. Output is in the form of a generic trajectory. The number of intermediates can be controlled with the
       -ninterm flag. The first and last flag correspond to the way of interpolating: 0 corresponds to input structure 1 while	1  corresponds	to
       input structure 2.  If you specify  -first  0 or  -last	1 extrapolation will be on the path from input structure x1 to x2. In general, the
       coordinates of the intermediate x(i) out of N total intermidates correspond to:

       x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1)

       Finally the RMSD with respect to both input structures can be computed if explicitly selected ( -or option). In that case,  an  index  file
       may be read to select the group from which the RMS is computed.

FILES

       -f1 conf1.gro Input
	Structure file: gro g96 pdb tpr etc.

       -f2 conf2.gro Input
	Structure file: gro g96 pdb tpr etc.

       -o interm.xtc Output
	Trajectory: xtc trr trj gro g96 pdb cpt

       -or rms-interm.xvg Output, Opt.
	xvgr/xmgr file

       -n index.ndx Input, Opt.
	Index file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -ninterm int 11
	Number of intermediates

       -first real 0
	Corresponds to first generated structure (0 is input x0, see above)

       -last real 1
	Corresponds to last generated structure (1 is input x1, see above)

       -[no]fityes
	Do a least squares fit of the second to the first structure before interpolating

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							g_morph(1)

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